FreeSurfer Voxels and Meshes

NIfTI and GIFTI are popular neuroimaging formats for voxels and meshes. However, FreeSurfer will often generate its own internal formats. This notebook displays FreeSurfer data.

from pathlib import Path

from ipyniivue import download_dataset

BASE_API_URL = "https://niivue.com/demos/images/fs/"
DATA_FOLDER = Path("images/fs")

download_dataset(
    BASE_API_URL,
    DATA_FOLDER,
    files=[
        "brainmask.mgz",
        "rh.pial",
        "rh.white",
    ],
)

Downloading brainmask.mgz...
Downloading rh.pial...

Downloading rh.white...
Dataset downloaded successfully to images/fs.

from pathlib import Path

from ipyniivue import NiiVue, SliceType

## Initialize Viewer

nv = NiiVue(slice_type=SliceType.MULTIPLANAR)

## Load Volume and Surfaces

nv.load_volumes([{"path": DATA_FOLDER / "brainmask.mgz"}])

nv.load_meshes(
    [
        {"path": DATA_FOLDER / "rh.pial", "rgba255": [64, 22, 222, 255]},
        {"path": DATA_FOLDER / "rh.white", "rgba255": [222, 194, 0, 255]},
    ]
)

## Configure Display Settings

nv.set_clip_plane(-0.1, 270, 0)
nv.set_mesh_shader(nv.meshes[0].id, "crosscut")
nv.set_mesh_shader(nv.meshes[1].id, "crosscut")

## Display Viewer

nv